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<h1>Pop-up Menus of MarvinSketch</h1>

<P>There are four pop-up menus (also called context or right-click menus) available in MarvinSketch:</P>
<blockquote>
<ul>
    <li><a href="#atom.popup">Atom Pop-up Menu</a></li>
    <li><a href="#bond.popup">Bond Pop-up Menu</a></li>
    <li><a href="#object.popup">Object Pop-up Menu</a></li>
    <li><a href="#edit.popup">Edit Pop-up Menu</a></li>
</ul>
</blockquote>
<p>These popup menus do not require the corresponding atom, bond or object to be selected,
however there are some <a href="#selection.popup">additional menu elements</a> that appear only when they are selected.</p>
<p>Please note that when a pop-up menu appears, it is usually the combination of these menus.
For example when selecting an atom and pressing the right mouse button, a popup menu appears that contains elements
of the Atom Pop-up Menu and the Edit Pop-up Menu. The elements are merged together to the displayed pop-up menu.</p>
    


<H3><a class="anchor" name="atom.popup">Atom Pop-up Menu</a></H3>
<P>The Atom pop-up menu appears when you right-click on an atom on
the canvas. It contains options for atom-specific activities.</P>
<TABLE CELLPADDING=5 cellspacing="0" class="grid">
<TR>
    <TH WIDTH=20%>
        <P>Menu Item</P>
    </TH>
    <TH WIDTH=80%>
	<P>Description</P>
    </TH>
</TR>
<tr>
    <td>
        <p>Stereo</p>
    </td>
    <td>
        <p>Assigns reaction stereo labels or enhanced stereo labels to atoms.
        See the <a href="../../sci/stereo-doc.html">Enhanced stereo specification</a> for details.</p>
    </td>
</tr>
<TR>
    <TD>
	<P>Charge</P>
    </TD>
    <TD>
	<P>Applies a <a href="../sketch-chem.html#charges">charge</a> between
        [-128,128] to the atom. Marvin will let you set any of these values on any atom, highlighting
        the Valence Errors in red upon completion. In other words, Marvin will
        allow you to set a charge of -5 on hydrogen, despite the fact that
        this is chemically impossible.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Valence</P>
    </TD>
    <TD>
	<P>Allows you to change the valence of any atom between [0, 8].</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Radical</P>
    </TD>
    <TD>
	<P>Sets the selected atom as a <a href="../sketch-chem.html#radicals">radical</a>.
            You can select the type of radical - monovalent, divalent,
        divalent singlet, divalent triplet, trivalent, trivalent doublet, trivalent
        quartet. The Off option removes the radical designation.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Isotope</P>
    </TD>
    <TD>
        <P>The <a href="../sketch-chem.html#isotopes" class="buttonName"
        >Isotope</a> submenu contains a list of the isotopes of the selected
        element, dynamically generated based on the selected atom. Select an
	isotope to set or change the isotope number or choose Off
            to reset the default atom type (no isotope).</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Map</P>
    </TD>
    <TD>
	<P>Set <a href="../sketch-chem.html#mapping">map</a> labels/identifiers on
            the selected atoms that do not change while altering the molecule.
            They are useful when dealing with reactions, and can be saved in SMILES and MDL formats.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>R-group</P>
    </TD>
    <TD>
	<P>Change the selected atom to an <a href="../sketch-chem.html#rgroups">R-group</a> label.
            R-groups symbolize alternative substituents.</P>
    </TD>
</TR>
<tr>
    <td>
        <p>Link Node</p>
    </td>
    <td><p><a href="../sketch-chem.html#link-nodes">Link node</a>
    specifies rings or chains of variable size.</p>
    </td>
</tr>
<tr>
    <td>
        <p>Attachment Point</p>
    </td>
    <td>
        <p>If the selected atom is part of a group (R-group definition or
        abbreviated group), you can specify an attachment point.</p>
    </td>
</tr>
<TR>
    <TD>
	<P>Delete</P>
    </TD>
    <TD>
	<P>Removes the atom from the molecule.</P>
    </TD>
</TR>

<TR>
    <TD>
	<P>Add Branch</P>
    </TD>
    <TD>
	<P>Adds a new bond with implicit hydrogen to the selected atom.
	This option is disabled for atoms that can have no more bonds.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Format</P>
    </TD>
    <TD>
	<P>Change atom drawing properties.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Add To My Templates</P>
    </TD>
    <TD>
	<P>Adds the selected structure to the "My Templates" group that appears in the Template Library and on the Advanced Templates Toolbar.</P>
    </TD>
</TR>
</TABLE>


<h3><a class="anchor" name="bond.popup">Bond Pop-up Menu</a></h3>
<P>The bond pop-up menu appears when you right-click on a bond within
the molecule. It allows you to make a number of changes to the
selected bond.
</P>
<TABLE CELLPADDING=5 cellspacing="0" class="grid">
<TR>
    <TH WIDTH=10%>
	<P>Menu Item</P>
    </TH>
    <TH WIDTH=10%>
	<P>Submenu Items</P>
    </TH>
    <TH WIDTH="80%">
        <P>Description</P>
    </TH>
</TR>
<TR>
    <TD ROWSPAN=6>
        <P>Type</P>
    </TD>
    <TD>
        <P>Single</P>
    </TD>
    <TD>
        <P>Changes the selected bond type to Single.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Double</P>
    </TD>
    <TD>
	<P>Changes the selected bond type to Double.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Triple</P>
    </TD>
    <TD>
	<P>Changes the selected bond type to Triple.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Aromatic</P>
    </TD>
    <TD>
	<P>Changes the selected bond type to Aromatic.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Bold Single</P>
    </TD>
    <TD>
	<P>Changes the selected bond type to Bold Single.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Query bond types</P>
    </TD>
    <TD>
	<P>Changes the selected bond to a bond type (Single Up, Single
        Down, Single Up or Down, Double Cis or Trans, Double C/T or
	Unspec, Single or Double, Single or Aromatic, Double or Aromatic,
	Any) for use in a query.</P>
    </TD>
</TR>
<TR>
    <TD ROWSPAN=4>
	<P>Attributes</P>
    </TD>
    <TD>
	<P>Stereo Search</P>
    </TD>
    <TD>
	<P>Uses stereoconfiguration of specified double bond when this
	molecule is used as a query.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>In Ring</P>
    </TD>
    <TD>
        <P>Sets a bond property so that when the molecule is used as a
	query, the specified bond must be in a ring to score a hit.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>In Chain</P>
    </TD>
    <TD>
	<P>Sets a bond property so that when the molecule is used as a
	query, the specified bond must be in a chain to score a hit.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Reacting Center</P>
    </TD>
    <TD>
	<P>See <a href="http://www.chemaxon.com/jchem/doc/user/Query.html#reactingcenter">Reacting center bond</a> query feature description.</P>
    </TD>
</TR>
<TR>
    <TD ROWSPAN=2>
	<P>Align</P>
    </TD>
    <TD>
	<P>Vertical</P>
    </TD>
    <TD>
	<P>Orients the bond vertically.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Horizontal</P>
    </TD>
    <TD>
	<P>Orients the bond horizontally.</P>
    </TD>
</TR>
<TR>
    <TD colspan="2">
	<P>Delete</P>
    </TD>
    <TD>
    	<P>Removes the bond from the molecule.</P>
    </TD>
</TR>
<TR>
    <TD colspan="2">
	<P>Format</P>
    </TD>
    <TD>
	<P>Change bond drawing properties.</P>
    </TD>
</TR>
<TR>
    <TD colspan="2">
	<P>Add To My Templates</P>
    </TD>
    <TD>
	<P>Adds the selected structure to the "My Templates" group that appears in the Template Library and on the Advanced Templates Toolbar.</P>
    </TD>
</TR>
</TABLE>


<H3><a class="anchor" name="object.popup">Object Pop-up Menu</a></H3>
<P>
This menu appears when the context is a graphical object like Text, Bracket, or other Graphics.
</P><BR>

<TABLE CELLPADDING=5 cellspacing="0" class="grid">
<TR>
    <TH WIDTH=20%>
	<P>Menu Item</P>
    </TH>
    <TH WIDTH=80%>
        <P>Description</P>
    </TH>
</TR>
<TR>
    <TD>
	<P>Bring to Front</P>
    </TD>
    <TD>
        <P>Brings the selected object in front of all others.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Send to Back</P>
    </TD>
    <TD>
	<P>Places the selected object behind all others.</P>
    </TD>
</TR>
    <TR>
        <TD>
            <P>Delete</P>
        </TD>
        <TD>
            <P>Removes the object from the canvas.</P>
        </TD>
    </TR>
<TR>
    <TD>
	<P>Format</P>
    </TD>
    <TD>
	<P>Change object drawing properties.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Add To My Templates</P>
    </TD>
    <TD>
	<P>Adds the selected structure to the "My Templates" group that appears in the Template Library and on the Advanced Templates Toolbar.</P>
    </TD>
</TR>
</TABLE>

<H3><a class="anchor" name="edit.popup">Edit Pop-up Menu</a></H3>
<P>The Edit pop-up menu appears when you right-click on open canvas
space. In case there is an atom, bond or graphic object under the cursor, the appearing pop-up menu
contains the elements of the Edit Pop-up Menu merged with the pop-up menu of the selected element.<br>
Edit pop-up menu items include:</P>

<table cellpadding="5" cellspacing="0" class="grid">
    <tr>
        <th width="20%">Menu Item</th>
        <th width="80%">Description</th>
    </tr>
    <tr>
        <td>Add/Remove Explicit Hydrogens</td>
        <td>Switches explicit H atoms to implicit ones and vica versa. Explicit hydrogens are displayed with atoms joining its neighbor while implicit hydrogens are displayed by atom symbols only.</td>
    </tr>
    <tr>
        <td>Add/Remove Map Atoms</td>
        <td>Adding atom maps is an automatic assignment of map numbers to all selected atoms of a reaction by using the automapper tool.</td>
    </tr>
    <tr>
        <td>Add/Remove Data</td>
        <td>Attach/Remove data like stoichiometry coefficient to the molecule.</td>
    </tr>
    <tr>
        <td>Add/Remove Absolute Stereo (CHIRAL)</td>
        <td>Sets/Removes chiral flag for the molecule.</td>
    </tr>
    <tr>
        <td>Add Multi-Center</td>
        <td>Add a multi-center attachment point representing a group of atoms.</td>
    </tr>
    <tr>
        <td>Add Position Variation Bond</td>
        <td>Create a variable point of attachment to represent a connection point to a group of atoms.</td>
    </tr>
    <tr>
        <td>Edit Data</td>
        <td>Changes a previously attached data like stoichiometry coefficient of the molecule.</td>
    </tr>
    <tr>
        <td>Link Node</td>
        <td>Specifies query structures containing rings or chains of variable size.</td>
    </tr>
    <tr>
        <td>R-Logic</td>
        <td>Allows setting additional R-group conditions such as occurrence, rest H and if-then expressions to R-groups in the R-logic dialog.</td>
    </tr>
    <tr>
        <td>Merge Reaction Fragments</td>
        <td>Merge the selected fragments to a reactant, product or agent.</td>
    </tr>
    <tr>
        <td>Split Reaction Fragments</td>
        <td>Split the previously merged reaction fragments.</td>
    </tr>
<TR>
    <TD>
	<P>Format</P>
    </TD>
    <TD>
	<P>Change atom and bond drawing properties.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Add To My Templates</P>
    </TD>
    <TD>
	<P>Adds the selected structure to the "My Templates" group that appears in the Template Library and on the Advanced Templates Toolbar.</P>
    </TD>
</TR>
</table>

<h3><a class="anchor" name="selection.popup">Pop-up elements upon Selection</a></h3>

<TABLE CELLPADDING=5 cellspacing="0" class="grid">
<TR>
    <TH width="20%">
	<P>Menu Item</P>
    </TH>
    <TH WIDTH=80%>
	<P>Description</P>
    </TH>
</TR>
<TR>
    <TD>
        <P>Recent</P>
    </TD>
    <TD>
	<P>The <B class="buttonName">Recent</B>	submenu contains a list of
        atoms and templates previously placed on the canvas. It does not
        include recently used bonds. You can change the drawing object by
        selecting one of the items in this list.</P>
    </TD>
</TR>

<TR>
    <TD>
	<P>Cut</P>
    </TD>
    <TD>
	<P>Removes and copies the selection to the clipboard.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Copy</P>
    </TD>
    <TD>
        <P>Copies the selection to the clipboard.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Copy as</P>
    </TD>
    <TD>
	<P>Copies the selection to the clipboard in the specified format.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Paste</P>
    </TD>
    <TD>
	<P>Inserts the contents of the clipboard at the location of the cursor, without replacing selection.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Select All</P>
    </TD>
    <TD>
	<P>Selects the structure being on the canvas including all fragments and graphical objects.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Create Group</P>
    </TD>
    <TD>
        <P>Creates an abbreviated Group from the selected substructure.
	See the <a href="../sketch-chem.html#sgroups">S-groups</a> section for
        more information on creating and using Groups.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Flip</P>
    </TD>
    <TD>
	<P>Flips the structure on the canvas. The submenu allows you to
	choose horizontally or vertically.</P>
    </TD>
</TR>
<TR>
    <TD>
	<P>Mirror</P>
    </TD>
    <TD>
	<P>Flips the object horizontally, inverting
	tetrahedral stereochemistry. The submenu allows you to
	choose horizontally or vertically.</P>
    </TD>
</TR>
</TABLE>

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